Doctor Who - Massive Effect
by efhb1994
Summary: [REWRITE] - There's an ancient legend in the universe which has surpassed everything, lived on from generation by generation. The legend of the Doctor, which has influenced the Galaxy. From the ancient Krogans of Tuchanka to the founding of the Citadel Council. He's now needed more than ever as the Reaper War begins. Question is, can the insidiout plot behind it all be prevented?
1. Prologue

_There's an ancient legend in the universe which has surpassed everything, lived on from generation by generation. The legend of the Doctor, which has influenced the Galaxy. From the ancient Krogans of Tuchanka to the founding of the Citadel Council._

 _The Doctor has always been there, but he has been forgotten. Like most things, trace of him vanished and people's faith in his existence waned. The legend became a myth, nothing more than tall stories remained._

 _However, for those who know where the look. The so-called myth and legend. Is quite real. In the year of 2186, Doctor Liara T'soni will stumble upon a discovery while searching the Prothean Archives._

 _The Milky Way Galaxy was on the precipice of war. The Reapers were coming to continue with their cycle of destruction. The need has never been so dire. Earth, Humanity, all sentient life in the galaxy now needs the Doctor. For without him, the probability of a victory against the Reapers is slim at best._

 _The Reapers were coming, they had laid waste to the Batarian Hegemony and was now underway towards the Systems Alliance territory. For Earth._

…

Liara T'soni skimmed through the data on the display with a direct feed from the Prothean Archives. Admiral Hackett had asked for her specifically, not only due to her degree in Xenoarchaelogy but also that she was a close friend and ally of Commander Shepard. She believed – no, she knew that the Reapers were coming. Six months ago, he had destroyed a mass relay and by consequence; all three hundred thousand batarian colonists in the Aratoht system had perished.

It appalled her, the very notion to sacrifice an entire system. Just to slow the Reapers down. Yet she knew that Shepard had no choice, that there hadn't been another way. She couldn't begin to fathom the guilt weighting Shepard down after having been forced to make a impossible decision. However, would it be worth it in the end? Liara didn't know but she wasn't about to roll over and waste time. The Archives still held troves of information. There had to be something here which could help.

She then paused as she noticed something odd in the datastream. Her brows were perked, the data she was now examined was a song. Why would a song be in a prothean archive? It was easy to translate, like if it translated itself.

.

I cross the void beyond the mind

The empty space that circles time.

I see where others stumble blind

To seek a truth they never find.

Eternal wisdom is my guide.

I am the Doctor.

.

Through cosmic waste the TARDIS flies

To taste the secret source of life.

A presence science can't deny

Exists within, outside, behind

The latitude of the human minds.

I am the Doctor.

.

My voyage dissects the course of time

"Who knows?" you say

But are you right?

Who searches deep to find the light

That glows so darkly in the night

Toward that point I guide my flight.

.

As fingers move to end mankind

Metallic teeth begin their grind.

With sword of truth I turn to fight

The satanic powers of the night.

Is your faith before your mind?

Know me. Am I, the Doctor?

.

Liara was confused, now fidgeting as a question came to her mind. Unknown to her, it was the first question, the oldest question in the universe.

Doctor Who?

…

 **Author's Note:** Thank you for reading, I hope you enjoy the beginning of a grand adventure. All content featured in this story is respectively owned by their writers, publishers and composers.

That includes the song, "Who is the Doctor" which was originally sung word by word; by no other than John Pertwee to the classic doctor who theme in 1972.


	2. Introductions

Commander John Shepard sat yet again in an interrogation room in Vancouver. It was a bland room with a single table and two chairs. It's been six months since the destruction of the Alpha Relay. John was a man of an athletic build with a cranium which fit the really short haircut. A stubble running dowm his jawlines and chin, he've not had the luxury of a decent shave. He was dressed in a casual garb while seated on the chair facing the doorway, his wrists had been cuffed and magnetically connected to the table who's legs where pinned to the floor.

James Vega was outside as per usual, guarding his assigned prisoner. The Alliance Marine was a stout and heavily built man from the pacific whom was casually dressed with a blue t-shirt and proudly displaying his dog-tags on his chest. The Lieutenant didn't like that they put Commander Shepard once again in interrogation. Hadn't the brass got enough for the preparation of his trial?

His train of thought stopped as a man stepped before him, dressed in a blue trench-coat, a wide and sparkling smile and fantastic brown hair. The man extended his hand to the marine whom grasped it with a perplexed expression.

"Captain Jack Harkness, Alliance Intelligence. I'm here for Shepard's interrogation." The man said in a smooth voice.

"Lieutenant James Vega, Alliance Marine Corps." He responded, apparently keeping himself in line before the oddly dressed Captain. He seemed like a sleeky bastard with those pearl-white teeth and loop-sided smile of smug confidence and almost wiggling eyebrows.

"He's right inside. However, I'd like to see some credentials. You never know about whom you can trust."

"That's a good attitude, James. Can I call you James?" asked the man while forwarding the credentials with his omni-tool.

 _Authorization Code Confirmed  
Captain Jack Harkness, N7  
UNIT, Alliance Intelligence, Torchwood_

James paused, what the hell was Torchwood? He looked back up at the seemingly lighthearted and actually quite charming man. Really, he was a N7? He snapped to attention and saluted. "Go right in, Captain." James said as he the charming Captain over the threshold.

 **...**

The man entering the interrogation chamber wasn't what Commander Shepard expected, he wasn't even dressed in an Alliance service uniform. All the same, unlike the preceding interrogators. This one was smiling widely as he sat down in the chair opposite of Shepard. The Commander couldn't help but feel that the man was oddly familiar.

"Commander John Shepard, I must truly say that this is a tremendous honour. I still remember what you did at the Skyllian Blitz, I was there in fact – saw you first-hand in action."

It clicked to Shepard whom he was speaking to. "I remember you, Jack Harkness. Alliance intelligence?"

Jack Harkness returned a vague nod. The door had closed behind him as he then noticed how it then was locked as well. Another precaution. "Excuse me for a minute." Jack Harkness said as he lifted his omni-tool on his left wrist as he pressed a button which sparkled everything.

"There, now we can talk in private." Said the man after his rather orthodox act, he had disabled the surveillance in the room. This didn't sit right with Shepard.

"About what?" asked Shepard in a mistrusting tone. "Are you with Cerberus?"

"Goodness no, Torchwood." Jack responded with the same charming smile as he casually leaned back in the chair opposite of him. "Never heard of it." The commander responded.

"And you would never had to if this wasn't necessary." There was a reason why those in the Alliance Intelligence were called spooks, you never know what they were truly doing in the shadows. Could Torchwood be the Alliance Black Ops which replaced Cerberus once it went rogue? Did Anderson, or even Admiral Hackett put him up with this? "We actually came before Cerberus, instituted back in 1879 by Queen Victoria."

Shepard perked a brow, both confused and puzzled, it was like he knew what he thought like. "Our purpose were back then to protect the British Empire from Extraterrestrial threats."

The Human Spectre listened, slightly intrigued since he wasn't aware of anything that Jack Harkness told him. "We act outside the government and beyond the law as her royal majesty had decreed. Arming the human race for the future. Today, we're a secret branch of Alliance Intelligence but our purpose remains the same. To protect the human race."

"And why are you telling me this?" Shepard was skeptical, what if this was a ploy of the Illusive Man?

"Because we believed you about the Reapers even when the brass and the council didn't." said Jack, now having Shepard's absolute attention. Jack gave out a laugh. "I knew that would get your interest. Now, here's the thing. We've prepared as much as we can without the brass knowledge, you know. Safehouses. Security bunkers. Holdouts for a resistance should the Reapers ever invade. Well, Anderson knows ofcourse, I told him myself not so long ago."

Shepard listened, this was the best news that he've heard for a good while now. "You're not alone in this fight, Commander. In fact, your shadow broker friend is right now at the Prothean Archives on Mars trying to find a way to fight the Reapers."

Shepard blinked, twice. He knew about Liara being the Shadow Broker. How the hell did he found out? He dismissed that thought since Jack was obviously not a hostile. Frankly quite friendly. He's glad that he atleast has some allies beyond his friends and usual contacts.

"Your trial is less than a week away, Commander. I'd wish you luck and… one other thing." Said Jack Harkness as he rose from his chair, he had done what he came to do. "I'll be joining Lieutenant Vega in the security detail to guard you." Jack said and gave him a michievious wink before the door opened behind him with Alliance personal staring with arms drawn rather quizzically. The man turned casually around to face the armed soldiers.

"Only took you six minutes. I can honestly say that I'm disappointed. Either way, Captain Jack Harkness, Alliance Intelligence. Everything is under control. Just a security check." The man said, the additional security response lowered their M-3 Predators. Jack then just walked by them as he waved his farewell to Shepard.

Shepard simply stared. This had been the most ludicrous but hopeful event which had happened to him in six months. He couldn't help but crack into a vague grin while James Vega escorted him back to his quarters.

 **…**

A piece of chalk squeeked as the tip was pressed against the drawing board. The Doctor's focus was absolute as he wrote the most elaborate equations which would leave a human physicist dumbfolded and ask him what it was in confusion like an infant wanting an explanation of something they couldn't comprehend. Worst of it was that he's bored. He was hoping to somehow pass the time. To distract himself but inevitebly found himself thinking about Riversong. He shook his head and walked down the steps to the center dias. He cranked a lever as the center column rose as the engines wheezed the groaning sound while the TARDIS navigated through the time vortex. Nardole was trying to solve a cross-word in a newspaper. "Alright, where are we off to this time?" The timid and rounded man asked as he looked up at the Doctor.

"I've no idea." The Doctor said before he walked through the door. The air tasted artificial, like it's been recycled through the filters of a sophisticated life-support system for thousands and thousands of years. He looked about, he had landed on a walk way over some pond. Given the size, the station he was on must be massive. The design was familiar, as was the pond and that statue of a Krogan. He was on the Citadel.

"Ehh, Doctor." Nardole spoke, the wary tone in his voice brought him back to the present. C-SEC had them surrounded and trained their mass accelerated rifles at him. Terrific, what was it with people aiming guns at him? He spotted Turians, Humans, An asari and a few Salarians. He spotted an older man whom had the grizzly grit of a veteran of sort. His curt demeanor as he approached them like an authority figure, atleast he wasn't a soldier but he was without a doubt in command of the C-SEC personnel present.

The Time Lord though couldn't help but scowl at the approaching C-SEC Officer and it seemed to give him some pause. His arcing and brushy eyebrows did add an intimidation factor of his scowl. "Hello, I'm the Doctor."

"Doctor who?" Is all he got as a respond from the C-SEC Officer before he shook his head. "Nevermind, I'm Commander Bailey of C-SEC. And I want to know how you got inside the Citadel with that blue box of yours." The Doctor simply procured his psychic paper from his pocket and showed it to Commander Bailey.

"Permission from the Council eh? That's funny because they don't use papers for permits of any kind." Uttered the Commander. "Doctor, you're hereby under arrest for avoiding citadel customs and smuggled an unidentified vehicle onto the station and on top of it, posing as a Council Offical. I'll be fair though and give you one chance to explain yourself." Commander Bailey responded rather quizzically. This was all too odd for him.

"I got a better idea, why don't I show you?" The Doctor responded before turning around, making way for the box. The C-SEC officer look like they're ready to open fire but Commander Bailey hold his hand up. He wanted to see what the Doctor had to show him. "Nardole, would you care to give me a hand." The man timidly walked over to the Time Lord whom procured his TARDIS Key, it wasn't until he opened the door and pushed Nardole through and slammed the door in the face of dumbfolded C-SEC. A loud click was heard as the TARDIS door locked and the C-SEC Officers opened fire before Commander Bailey could order otherwise.

Yet all the projectiles did was bouncing off the Tardis. Commander Bailey looked baffled, the weapons were modified with piercing rounds. It should've shredded the wood. They saw the lamp on the top of the box to start flashing as they heard the same wheezing and groaning sound which had alerted them. The box was fading away from existence before them and just vanished as the sound became ever most distant. All of them stared in wonder.

"Seal off the perimeter and direct all traffic to the other side of the presidium. Don't let anyone get close to the site, along call all science geeks we got." Barked Commander Bailey to his personal. He wasn't happy with the outcome, neither was he happy that his men had opened fire without his consent.

All the same, he'd have to inform the Council of what just had transpired, they'd want to hear about that blue box, and this mysterious Doctor.

 **…**

"Blimey, that was close." Nardole complained. The Doctor was more annoyed than surprised by this C-SEC pointing guns at him. Then again, he was curious as he walked over the central dial and flipped a few more switches before the Tardis materialized again. A human was Commander of C-SEC implied that the Systems Alliance had gained a seat on the Citadel Council. The Doctor couldn't help but grin, it's been a while since he visited this time period. Yet he was puzzled by the more aggressive nature of C-SEC. Something was off. Which was why he was now inside the Citadel's Secret Archive. It was evidently well after closing hours. The moment he exited the TARDIS, with a flick of his wrist, his sonic screwdriver buzzed and sent the security intoa loop during the duration of his stay.

The Doctor found himself standing infront of a circular chamber which showed a holographic projection, the Tardis as perusual had taken him where he was needed. He flashed the screwdriver which started the holographic projection to move. It displayed with incredibly detail about an attack on the Citadel which was executed three years ago. Apparently a rogue spectre and an army of geth had been behind it but what really got the attention was what the archives referred to as a Geth Juggernaut which was two kilometers in height and six arms. It was massive. It was also wrong. He knew of the Geth and the circumstances of the Morning War. It was a pity, but he couldn't solve all of their problems. Yet the Doctor knew well enough that the Geth couldn't have built that. It was impossible.

The Doctor was perplexed as something rubbed him the wrong way. It was as if time itself was wrong. He could feel it now and he quickly dashed off again and entered the TARDIS. The Time Lord was at the central dias when he snapped his fingers, causing the doors to close as if on its own accord.

"Time is wrong. Someone is interfering and I'm not talking about me." The Doctor voiced with a determination, he glanced over to Nardole. "How would you like to visit the first human Spectre on Earth, 2186?"

"I'm not very fond of ghosts, Doctor." The Timid man replied, the Doctor couldn't help but fathom if Nardole was put in a position of power. He was pretty sure that the galaxy would implode. The Doctor turned a knob and cranked a lever. The wheezing and groaning sound of the TARDIS granted him a moment of peaceful harmony, he loved this part.

 **…**

A man sitting before clear but vibrant room with many mirrors, facing a virtual desktop and controls as he gazed out at the blazing red sun as he viewed the security footage from the citadel through his radiating and artificial eyes. He was well-clad and took a long drag from his lit cigarette. He was smiling, he had just witnessed the appearance of something extraordinary, an indestructible blue box which could move without trace or effort by a mass effect field.

The Illusive Man had read the report from his inside source of C-SEC. A man had showed up out of nowhere on the Presidium in a blue policebox. Then vanished without a trace.

He had called himself The Doctor. He'll have to direct some of his resources to dig up something more about the man.

His research team worked around the clock ever since Shepard had destroyed the Collector's base six months ago, he had used his resources to salvage what he could. Including the remains of the proto human-reaper which was now aboard Charon Station.

He was disappointed with the defection of Operative Lawson and Taylor. He expected as much of Jacob, but Miranda? She had taken it too far and developed feeling for the Commander. His latest report suggested was that they had been – entangled in a relationship as well.

Maybe he could turn this around, the Commander did have a past relationship with Gunnery Chief Williams who now had ascended to the rank of Lieutenant Commander. His mischievous and smug grin was kept in moderation. Pleased to say the least as he now adjusted his already deeply developed plans.

Looking out the window as he waved the report away, taking another drag from his cigarette before pressing a button on the interface. "Operative Reinfeldt, personally direct a token of our intelligence sources to investigate the anomaly of the Doctor and his blue police box."

Reaching out as to grasp his whiskey glass with American bourbon, taking a well drag out sip as to enjoy the flavor as a green light signaled from the interface along with a beep. His command was received and acknowledged. His smile never leaving his face as he gazed into the red star, imagining humanity's ascendance to greatness.

 **…**

 **Author's Note:** A friendly reminder that I appreciate any kind of constructive critic and suggestion which may improve the overall story. Furthermore, I wish you a grand morning, noon, afternoon or night whenever you've read through this chapter.


	3. Defense Committe

"So, Torchwood? What's it like?" James Vega asked the man opposite him in the cafeteria of the Alliance Headquarters in Vancouver. It was a nice view with a wide view of the skylines with many vehicles passing through inbetween the skyscrapers. It was pristine, clean and beautiful.

"Spetacular, we used to have this competitive rivalry with UNIT back before the Systems Alliance was formed and the two integrated." Captain Jack Harkness replied while dashingly smiling, "Shame about the Ice Warriors, the Protheans sent them on the run once they had wiped their planet."

James just shook his head, Martians? Yeah, right and the Reapers were real. The two of them had developed a sense of comradery which was founded on their mutual trust of Commander Shepard. James was glad that he wasn't the only one who trusted the Human Spectre. He wasn't sure if he believed what he said about the Reapers but the talk about the existence of Martians? That's just bullshit.

Still, he was still sure that Jack Harkness was checking him out, he was a sleeky bastard but a cool sleeky bastard if you get the idea. He was in a service uniform now while Vega still was dressed in his bunk shirt. It still was a good time to catch a break as it's been tense on the base for the last couple of hours. Something was apparently going on, that much was obvious.

"Did you know that people have the misconception that UNIT is the Military arm of Alliance Intelligence? In reality, the Alliance Intelligence and Alliance R&D are branches of UNIT." Jack inquired, seemingly at ease as he took a sip from his mug of coffee.

"No, I had no idea actually." James replied in all honesty. "Where does Torchwood really like though?" The misdirection which Harkness made didn't fly over his head, well almostly didn't fly over his head.

"I'm sorry James, that's classified." Jack answered, "What I can tell you though that we're monitoring threats to humanity and its allies. Believe me, there's a threat on the horizon to all of us." The way he spoke puzzled James. The implication wasn't lost to him, he was talking about the Reapers. If UNIT took Shepard's claims that seriously to consider it a threat. Then they've been fools of ignoring Shepard's warnings for the past three years.

Their Omni-tools chimmed with an alert. Jack was already skimming through the message before James could even check his. The cheerful disposition which Jack had earlier evaporated. "The defense committee is in an emergency session and wants to see Shepard ASAP." They both rose from their respective seats, lunch break was over for them. They left the Cafeteria in quick strides, there was a increased amount of tension in the air as they moved through the corridors. Everyone seemed to be in a hurry. They promtply arrived to Shepard's Quarters, they trusted him well enough to put him under house arrest instead of locking him up in a brig. He did turn himself in afterall and was capable of breaking himself out if he wanted to.

James stood attentively and saluted Shepard once he had entered the room. "Commander." He announced. The Human Spectre turned about, having been looking out the window with a datapad in hand.

"You're not supposed to call me that anymore, James." The Human Spectre said, briefly looking up from a datapad. His eyes set upon him once he spotted the salute.

"I'm not supposed to salute you either." James retorted, Shepard conceded with a nod. "We got to go, the defense committee wants to see you."

Shepard perked a brow, "Sounds important." he said as heeasily let go of the datapad upon the bed and followed James through the door. Once out in the hallway, Shepard noticed the increased pacing of the Alliance personnel. "What's going on?"

Jack Harkness whom had waited outside, and walked a few paces behind them spoke up. "We've lost contact with everything beyond the Sol System." The answer made Shepard's expression to harden, glancing over his shoulder at Jack and nodded curtly as he followed James through the corridor. However it didn't take long for a familiar figure to meet them. A well-built black man in his late prime dressed in a pristine naval dress uniform with four golden stripes decorating each shoulder.

"Anderson." Shepard said in acknowledgement as they shook hands. Vega and Harkness saluted as per the military doctrine to address a superior officer with respect.

"You look good Shepard. Maybe a bit soft around the edges. How are you holding up after being relieved from duty?" Anderson said, a bit jovially.

"It's not so bad when you get used to the hot food and soft beds." He replied in good humor as they continued down the corridor.

"We'll get you sorted out." The Admiral replied with a faint smirk.

"What's going on? Why is everyone in such a hurry?"

"Admiral Hackett's mobilizing the fleets. I guess that word's reached Alliance Command. Something big is heading our way." Anderson answered, the tension in his tone was evidence enough for Shepard to know that something was up.

"The Reapers?" The question made Anderson stop in his stride and turn to face him. The tension was there alright, the jovial demeanor had changed to a more hardened disposition. It was mental preparation for the war to come.

"We don't know that, not for certain."

Shepard snorted, "What else could it be?" The question was valid, given the information they had. It was delusional to believe that something else other than the Reapers would be capable of severing the lines of communication from the Sol System to Arcturus Station and beyond.

"If I knew that—" The response was subtle enough, Anderson wasn't questioning that it was the Reapers. He was just dearly wishing it wasn't them.

"If it's the reapers then we're not ready for them. Not by a long shot." Anderson frowned as Shepard pressed his argument.

"Tell that to the defense committee." Anderson retorted, implying that Shepard didn't need to convince him. It was the Alliance Brass that he had to convince. They had started walking again, passing by a few clerks quickly skimming through their datapads. A few armed marines rushing to fortify choke points.

"Unless we plan to talk the reapers to death, the committee is a waste of time."

"They're just scared. None of them has seen what you've seen." Anderson replied, scowling at Jack as he exchanged a few words with a blond clerk whom blushed like a bride before striding off with a skip in her step. "You faced down to a reaper. Hell, you spoke to one then blew the damn thing up." Anderson continued, the tone in his voice was unmistakable. It was one of respect, of awe, of hope. "You've seen how they've harvested us, what they plan to do to us. You know more about this enemy than anyone."

"That why they grounded me? Took away my ship?" Sheppard snapped, some of his annoyance brought to the surface. They had stopped again in their path, the gleaming light of the sun shone upon them.

"You know that's not true." The response from Anderson was sharp, stern yet it was mild and considerate. A raised finger at him like if exaggerating a point. "When you blew the batarian relay, hundreds of thousands of batarians died."

"It was that or let the Reapers walk through our back door." He snapped back at Anderson, the reminder of how many lives had been lost because of him; over three hundred thousand batarians. They were all dead because of him and there was no excuse which would make up for what he've done.

"I know that, Shepard, so does the committee. If it wasn't for that, you'd had been court-martialed and left to rot in the brig." The reassuring tone of Anderson wasn't patronising or condescending. It was one of understanding of the guilt which was weighting him down.

"That, and your good word?" Shepard asked, the tension in his voice was evident. Not that he wasn't grateful, but he didn't deserve the special treatment. He would've to answer for his crimes, even if he was a Spectre.

"Yeah. I trust you, Shepard. And so does the committee."

"I'm just a soldier, Anderson. I'm no politician." Shepard argued, closely following his Anderson as they continued down the corridor towards the check point before the committee chambers.

"I don't need you to be either. I just need you to do whatever the hell it takes to stop the Reapers." The stern edge in his tone was one of a superior officer. Shepard couldn't argue with his logic, he was the First Human Spectre. He had more leway than any human had right to be. He knew that people looked up to him and saw as a hero, but he was still just a man. A red-headed clerk greeted them as they approached the check point. She was dressed in a blue naval service uniform and held a datapad. "They're expecting you two, Admiral." Her tone had been quite indifferent, cold and professional as they continued onwards.

"Good luck in there, Shepard." He and James shook hands while Jack gave him a reassuring smile. Shepard couldn't help but shake the feeling that despite the man's youthful appearance that he was older than he looked. That train of thought was interrupted once a familiar voice was heard.

"Anderson." That voice, his heart skipped a beat. He turned around to spot a woman dressed in blue armor emblazoned with insignia of the Systems Alliance Marine Corps. Ashley Williams still had her hair secured in a bun. They hadn't spoken since the aftermath of the Collector attack on Horizon. She had denied him her assistance when he asked for it, just because he was working with Cerberus to put a stop to the Collectors. They used to be in love, but the rejection didn't do him any favors. He put it behind to focus on the suicide mission through the Omega 4 relay.

His love for her had been firm, which was until Miranda Lawson thawed and ceased to be the Ice Queen he earlier knew. His thought process was interrupted when Ashley had turned towards him and said his name. "Shepard."

"Ashley." He replied, having mustered his confidence. He still had feelings for her but he couldn't act on those feelings. It was in the past.

"Lieutenant-Commander. How'd it go in there?" Anderson asked, gave Shepard time to collect himself.

"Shepard, I know it's a bit tough but right now. You got to focus." Jack Harkness whispered to him. Shepard knew that he was right. He could tell that his concern was genuine. Shepard had warmed up to the sleeky bastard whom somewhat reminded him a bit of the Illusive Man but with distinct differences in his demeanor and jovial nature. He still didn't trust him or Torchwood for that matter, however he didn't have the luxury to turn down help. Not with the Reapers right at their door.

"I can never tell with them. I'm just waiting for orders now."

Wait, Shepard caught up with Anderson had just said and snapped back to reality. "Lieutenant-Commander?"

Anderson glanced over at him, a perked brow. "You hadn't heard?" Evidently surprised that he hadn't heard of her promotion.

"No, I hadn't." Shepard responded curtly.

"Sorry, Shepard. It's been… well." Ashley said with a ghost of a smile. She still had feelings for him. He could tell by the way she subconciously fidgeted a bit. If he wasn't in another commitment, then he would've considered rekindled what they once had.

"It's okay, just glad that I bumped into you."

"Me too." She responded with a smile as the red-headed clerk returned as she motioned for Anderson and Shepard to come along with her as she called. "Admiral."

"Come on. You too Harkness." Anderson ordered, the two men followed the Admiral into the Committe Hall.

"You know the Commander?" James asked, the response was laced with sorrow and regret.

"I used to."

The Committe Chambers was pristine and in good condition, monitors on the wall and clerks going through various data through data-pads and omni-tools alike. At the far end sat the Admirals by an elevated desk facing them. The sun gleamed through the window behind them which only added to the prominence in their seats.

"Admiral Anderson. Shepard. Captain Harkness." Spoke the Admiral in the middle with a tone which carried weight and authority, Admiral Chen was in command of the Fourth Fleet which was orbiting Earth. To his left was Rear Admiral Fält, Head of Logistics for the Alliance Navy. Last but not least there was the head of UNIT to his right – Admiral Lethbridge-Stewart.

"What's the situation?" Shepard asked, there was no point in beating around the bush. The reapers were here and they might aswell cut to the case.

"We were hoping. That you would tell us." came the reply from Admiral Chen, the weariness in his voice was evident.

"The reports coming in are unlike anything we've seen. Whole colonies have gone dark. We've lost contact with everything beyond the sol relay." Admiral Lethbridge-Stewart added, out of all the Admirals present – she was the incarnation of self-control. A clerk handed Shepard a datapad which he skimmed through

"Whatever this is. It's incomprehensingly powerful." Admiral Fält continued, a sense of dread in his voice. Shepard looked up, the data was incontrovertible.

"You brought me here to confirm what you already know—" Shepard spoke as he looked up from the datapad. "The Reapers are here."

The whole hall fell silent, the clerk looked up from the monitors and other staff stopped in their track. All heads were turned towards him and Shepard knew that they were afraid.

"Then how do we stop them?" the voice of Admiral Fält broke the silence, the dread which was hinted was now more evident.

"Stop them? This isn't about strategy or tactics. This is about survival. The Reapers are more advanced than we are. More powerful. More intelligent. They don't fear us, and they'll never take pity on us."

"But… there must be some way." Admiral Fält continued, starting to lose his composure. Admiral Chen seemed more puzzled and in deeply in his own thoughts as his gaze was firmly set on him. Admiral Lethbridge-Stewart pursed her lips together, nodding for Shepard to continue.

"If we're to have chance of survival, we'll have to stand together." Shepard stated in a devoted determination.

"That's it? That's our plan?" The words blurted out of Admiral Chen's mouth in frustration. The tension hang in the air while a cough silenced them all.

"There are alternatives to consider." Admiral Lethbridge-Stewart spoke with everyone's attention firmly set on her. "In the Black Archives in London, we got a device which we can use to call for assistance from our most ancient and trusted ally."

Admiral Chen lofted a brow, "Our most ancient and trusted ally?" he replied sardonically. "Would you like to elaborate why this most ancient and trusted ally haven't aided us in the First Contact War or the Skyllian Blitz?"

"The Doctor isn't our babysitter." The curt reply silenced Admiral Chen. "We can't expect him to take care of all of our problems."

"The Doctor, Doctor Who?" Admiral Fält asked quizzically which Admiral Lethbridge-Stewart only answered with a smile which Shepard recognized as amusement.

"It's classified as per the Unified Secrecy Act, Admiral. We wouldn't want that information to fall into the hands of Cerberus." The Head of UNIT replied, the other Admirals reluctantly agreed with. Shepard could understand that they didn't like to be kept in the dark.

Admiral Anderson coughed, "Admirals, I think it's safe to say that Commander Shepard is free from all charges?" The three admirals turned their attention back to Shepard and Admiral Anderson and nodded.

"We've faith in Commander Shepard. Naturally a more thorough investigation will be conducted once the Reaper crisis is dealt with." Admiral Lethbridge-Stewart added, her eyes locking with Shepard's as she smiled before her eyes turned towards Jack Harkness. "Captain Harkness, you're to—"

However, before she could finish the sentence, the red-headed clerk interrupted dutifully but Shepard could tell that she was distressed. "Admirals, we've lost contact with Luna Base."

"The Moon, they couldn't be that close already."

"How'd they get past all of our defenses?" Admiral Fält uttered in disbelief. Admiral Chen narrowed his brows, his composure hardened.

"Sir, UK headquarters got a visual." The big screen changed and started to display the massive reaper in two kilometers height, who's blazing energy beams obliterated everything in its path. Holding the camera, an Alliance marine with a beret on his head looked a bit shock as he tried to show the footage but the signal was lost a few seconds after. The beam had incinerated him as well. Followed by that, footage from the Alliance News Network get caught in, displaying the horrors which occurred worldwide which got Jack Harkness' face to be wiped out as he said "Looks like the black archives are a no go."

Admiral Lethbridge-Stewart stared at the screen in disbelief herself, the first sign pass her composure. Shepard was fixated on it as well. Husks seemed to be crawling all over New York and the sky scrapers were falling apart.

"What do we do?" Admiral Fält spoke, his voice now seething with fear.

"The only thing we can, we fight or we die." The words were spoken firmly and with authority. They couldn't lose control now. There was no time to waste. War has come and there was no escape from it.

The admirals exchanged worried glances with one another, they nodded briefly in agreement while Anderson leaned in as to whisper into Shepard's ear. "We should get to the Normandy."

Then they heard it, like a crack of mechanical thunder and a big thud as a sovereign class Reaper descended from the sky and demolished the several blocks which was visible from the window. The Admirals turned around and stared in disbelief and horror. "Oh my god—"

The Reaper gave away a terrifying screeching sound as energy charged up in its red socket and unleashed an obliterating beam of destruction which continued to lay waste to the pavement, the park outside and the buildings with a clear intention of the target. Shepard shouted out "Move!" as he turned around with Anderson at his heels. Running away from the beam. What Shepard didn't expect was that Harkness was running towards the beam in a quick pace, vaulting the table as he proceeded to tackle Admiral Lethbridge-Stewart out of the way as the glass shattered and sent the admirals and the table flying. Getting caught in the blast instead of the Admiral.

Running for their lives as the tables flew over them and bounced over the door and blocked the doorway out of the hall, another beam was sent which sent Shepard flying to the wall. Hitting it dead on as he fell to the bench. Groaning and disorientated. Andersons' voice echoed in his eardrums which was banging like hell. "Shepard!" his eyes snapped open as he saw his mentor make his way to him. The once pristine service uniform was now ruined, covered with blood and concrete debris. "Shepard, come on get up."

He grabbed Shepard and pulled him up before handing him an M-3 Predator heavy pistol. "Here, take this." He turned around, making his way to the large cracked window. Barking an order. "We've to get moving."

"This is Admiral Anderson, report in anyone. Lieutenant-Commander is that you?" Anderson said, his finger against the earpiece plugged into his ear. Shepard was relieved that Ashley was alright while making his way through the debris towards Admiral Lethbridge-Stewart.

"What's your status?" asked Admiral Anderson over the com. Shepard gently reached out to assist Admiral Lethbridge-Stewart up on her feet. "I'm alright, thank you. Shepard." She said in a resolute manner before she got up to her feet. Shepard's gaze turned towards Jack Harkness who was caught dead on in the blast. While everyone else was terrified and ran for cover, he had run to save a life. That was courage beyond the call of duty. Shepard sighed, walking over to check on Jack Harkness and retrieve his dogtags. However, what he discovered amazed him. Harkness was still alive.

"I can't raise the Normandy. You'll have to find her. We'll meet you at the landing zone, Anderson out." Anderson's voice echoed in the. Jack was groaning, his blue naval service uniform in ruins, his skin now had a most gruesome complexion. Shepard didn't understand, how could Harkness still be breathing?

"That hurt like hell…" Jack cursed, he needed medical attention but they couldn't stay here. Shepard moved to lift up the man.

"Hold on, we'll get you to the Normady for medical attention. Admiral, you too." He commanded, an order which they complied with. Anderson took point as Lethbridge-Stewart watched the rear. Shepard, carrying the severely injured Jack Harkness out the window to behold the beautiful city of Vancouver to be caught in the terrors of war. No, the terrors of an interstellar harvest. All the while over his shoulder Shepard could hear Jack Harkness introducing himself to Admiral Lethbridge-Stewart in a cheesy way, ignoring the fact that he was badly injured. He was wrong when he thought that nothing could surprise him anymore.

 **…**

 **Author's Note:** There we are, people may have noticed the differences of this story and the last one. I would like to explain a few things. Firstly, yes this story features the 12th Doctor instead of the 11th. Secondly, I hit a writing block in my previous story due to me (stupidly enough) decided to add the Burning Legion into the whole mix. A mistake which will be avoided in this version. Thirdly, I would like to apologize in advance that like my other stories, the updates will be irregular. Finally, consider the cover image to be a placeholder since I no longer have access to image editing software.

Nevertheless, the game is afoot. The Reaper Wars has begun. Like in the previous story, "Miracle Day" never happened.

A friendly reminder that I appreciate any kind of constructive critic and suggestion which may improve the overall story. Furthermore, I wish you a grand morning, noon, afternoon or night whenever you've read through this chapter.


	4. Dawn of the Reaper War

The Doctor kept scowling at the monitor, the data procured from his scans flickering before his eyes in gallifreyan digits and symbols. The TARDIS had left the time vortex on its own accord in Earth's Orbit. It only took a moment to discover why. Earth was being invaded by highly-advanced machine race of synthetic-organic starships. hybrids _._ The mere thought was puzzling yet he couldn't afford to linger on it. It was time to act. He yanked a lever as the TARDIS wheezed and groaned as it propelled itself through real space. He switched for a visual image, the size of the invaders' vessels were distinctly different from anything he had ever seen before. Colossal in size, oozing with impossible readings. A gnawing sensation in his mind told him that they were wrong. "What are you?" The Time Lord murmured.

"Looks like giant squids to me. Those big ones." Nardole pointed out. The Doctor was about to argue when he noticed the metal appendages. They did remind him of giant squids.

He yanked a lever as the TARDIS wheezed and groaned, propelling itself through real space. The Doctor flicked a switch with his free hand as he spoke through an open-line; "Hello, Hello. Big oozing mechanical squids." the tone of his voice was deceptively lighthearted, yet it didn't take long for that tone to change. "I'm not sure that you've heard of me but I'm the Doctor, and that planet is under my protection." He continued, his tone was firm and hard like a serrated edge of steel. A few of the invading ships broke from orbit at intercept course for the TARDIS.

"We know of you, Doctor." replied a harsh voice which was worse than grinding a course surface against metal. "You cannot stop the harvest." The Doctor tensed, did he just called this attack as a harvest? Harvest implied that this wasn't a war to them. No, this was a means to an end. Wait, hybrids. They harvest for resources, in this case humans but for what, genetic material? Pure biomass? Regardless, they couldn't have it out on humanity alone. No, harvesting one species wouldn't be sufficient. This was a harvest on a galactic scale. He snapped out of this contemplation when he spotted that some breaking orbit with its metal appendages expanded into digits ready to grasp the TARDIS as a red gleam pulsates at its center as if priming its weapons.

"Then you've made your intentions perfectly clear." The Doctor replied with indignation, "If you know of me. Then you should know of what I'm captable of." There was no response and the machines doesn't seem to slow down in its approach. The Doctor cut the line, "So be it."

There was evidently no reasoning with these hybrids. They were monsters and it was up to him to stop them. He began to manuveur the TARDIS through real space, in the one direction no one expected him to – directly into the jaws of the beast. The TARDIS spun as it propelled through the real space at accelerating speed. In comparison, the Force field of the TARDIS was like a brick and the alien vessal; a piece of glass wrapped where the kinetic barriers might aswell be an sheet of tissue paper. Sufficient to say, the TARDIS went straight through the alien vessal, compromosing the eezo core which conaequently made it collapse on itself. The Doctor harbored no regrets, these things were no better than Daleks. The scans from earlier suggested that they were numerous and assaulted every major city simultaniously.

The Doctor didn't like this, this was something new and not something he fully understood. Yet he was determined to find a way. A way to win.

 **…**

Heart pounding, Jack felt how his body recuperate from the blast. "Shepard, put me down." He said as they walked at the rooftop. "We're not leaving you behind, Harkness." He snapped back and Harkness couldn't help but grinning. "Trust me, I've lived through worse. Put me down, now." He said in a trembling but a voice which held authority.

Jack grunted as he got off Shepard's shoulder, leaning down as he cursed while trying to overcome the pain which seared through his body. He started by tearing off his clothes. He had no use for them anymore and they were now annoying at best, not good looking at all. Eyebrows raised as he now presented himself completely naked, Harkness could tell that this was ludicrous for all of them. Stretching his limbs as he got up to his feet, gritting his teeth as he had once again returned from the dead.

They kept moving, all the others seemingly tried to avoid looking at Harkness while his manhood was loose from his underpants. They found a group of dead marine which were armed with M-8 Avengers. Without hesitation, Jack reached out to grab one from one of the dead soldiers.

This was World War II and the Skyllian Blitz all over again, but combined and far worse. Even on par with Game Station with the Doctor and Rose. They now found what had killed the marines, Reaper ground forces. He was quick to provide covering fire for the human Spectre and the Admirals but husks was approaching them from all sides. His shots were precise and remarkable accurate as it shredded through the enemy. He had loads of training and practice since he first joined Torchwood in the middle of the nineteenth century; not to forget mentioning that he passed the N7 Program which was by itself an achievement.

He had ripped all over his clothes, standing firmly naked with the weapon in hand which had him laughing at first. All the same, his body was restoring itself. The cells repaired themselves as the gruesome complexion slowly faded away. Immortality had its perks afterall. The thought of immortality brought back to what had caused it. Bad Wolf. He missed Rose but he missed the Doctor even more. After everything he has been through, he had a responsibility to protect humanity and his allies. That's what the Doctor would've done and despite everything going on, he didn't regret a thing. Sure, it seemed hopeless but he wasn't about to give up. Not now, or ever for that matter.

A Dreadnaught exploded, the kinetic shock from the blast threw them off their feet. Sending them crashing down the wall and delivered them down to what remained of the pavement beneath them. Fortunately, Shepard saved their hides through a sleight of hand with his biotics. Dampening their fall.

They got back up, it seemed like hell had descended upon them. Their line of communication broken as they struggled through the debris. They found two soldiers, one of them injured whom despite the terror couldn't help but be startled by the naked Captain. Jack playfully winked at the one in the blue berret whom strangely enough reminded him of Ianto. That line of thought was interrupted when Jack spotted the most disgusting being which he had laid his eyes on for the past centuries. Batarians deranged and altered to small moving mountains of flesh with glowing artificial eyes and an arm replaced with a human limb with a cannon where their should be a hand. They took cover when abominable things opened fire upon them. Shepard made of his biotics and shredded them to pieces. They fought their way through the Cannibals. They had reached a radio next to a crashed trident. Anderson immediately got to it and managed to establish a connection to the Normandy. They were in dire need of extraction. All they had to do was to hold their ground and stick to the landing zone.

It would take a while, Jack would've doubted the odds of their survival if he hadn't read all the files on Shepard and his known associates and maintained surveillance for the past couple of years. They had a chance to survive, there was always hope despite the dark cloud covering them. Flight Lieutenant Moreau was the best damn pilot in recorded human history. Even the humans of the fifty first century admired the man explicitly for his skill.

The cannibals and husks were closing, Shepard was evidently a priority target. They held their ground but they were running out of thermal clips. Jack made every shot count, quite literally. He wished that he still had his trusty Compact Laser Deluxe up in his prostate but he had to get rid of it. Admiral Lethbridge-Stewart held up her Omni-tool, waving it as electrical surges crippled many of the approaches. The legacy of the Brigadier was evident in how she fought, determined to fight for Earth until her last breath. The fire support she provided with the M-3 Predator along with her Tactical Cloak granting them an edge and allowed them to hold their ground.

A large group of cannibals were aiming at them as they were firing volley after volley of suppressing fire. Pinning them down as the husks came ever closer. It felt a bit hopeless until the Normandy flew overhead and blasted the remaining reaper forces to smithereens.

The shuttle bay opened, a few Alliance Marines lead by Ashley Williams was taking position on the ramp to provide covering fire while they extracted. Shepard was first of them on the ramp, a fresh thermal clip tossed to him which he loaded into his M-8 Avenger to assist with covering the others. Admiral Lethbridge-Stewart was quick to join them, her blue service uniform now tarnished and worse for wear. Yet what really raised eyebrows was the naked Captain Jack Harkness when he came aboard, smiling michieviously and winked to one of the marines whom quickly averted his gaze.

Anderson though still stood there, the expression on his face spoke for itself. _I'm not going,_ Shepard shook his head. "No."

The Admiral bristled, gesturing towards the besieged city of Seattle-Vancouver. "You saw those back there. There's a million more like them. And they need a leader."

"We're in this fight together, Anderson!" Shepard shouted back, he wasn't keen on leaving Anderson behind. He didn't want to lose him like he had lost Kaiden Alenko.

"It's a fight we can't win, not without help." Anderson snapped back, "We need every species and all their ships to even have a chance to defeat the Reapers." Anderson barked to Shepard as he continued with his tough mentoring love for his protégé. "Talk to the council. Convince them to help us."

"What if they won't listen?" Shepard asked. Anderson quickly responded. "Then make them listen. Now go, that's an order!"

"I don't take orders from you anymore, remember?" Anderson reached for his pocket, tossing him a pair of dogtags. They were caught fluidly by Shepard which recognized them as his own.

"Consider yourself reinstated, Commander." The voice of Admiral Anderson was one which broke no argument. His eyes telling Shepard that he had to do this, because no one else could. "You know what you've to do."

"I'll be back for you and I'll bring every fleet I can." Shepard said with great reluctance. He was about to turn about before stopped himself and added. "Good Luck."

"You too. Shepard." Anderson responded as he turned around, dashing off in a quick and rapid series of vaults and dashing among the city ruins. Two Kodiak shuttles in the distance were being loaded with civilians. Shepard spotted the kid he saw playing earlier in the garden and then in the ventilation duck. His heart fell when he spotted the beam which obliterated the shuttles. All of those civilians, dead

Shepard looked away, unable to look at the devestation anymore as he continued to walk further in. The Shuttle Bay doors closing behind him.

Shepard turned to face Harkness. "Go and get dressed." he ordered while James starting to walk straight towards him.

"What the hell is going on? Where's Anderson? Where are we going?" Shepard frowned, didn't he know better than to question a superior officer. Apparently James didn't like being ignored. "Hey!"

"We are leaving." He snapped back at the Lieutenant while walking around to get to the console.

"Leaving?" James exclaimed in frustration and disbelief, Ashley Williams didn't seem to like it either but was composed enough to remain disciplined.

"Anderson wants us going to the Citadel. Getting help for the fight." Shepard responded as he proceeded to make a quick inventory of what they were stocked with.

"Bullshit, he wouldn't order us to leave." Lieutenant Vega objected, obviously angry that they were making a strategic withdrawal.

"We don't have a choice! Without help, this war is already over." Shepard's sharp voice put an end to the ranting, or so he thought while scrutinizingly staring at the marine.

"Forget it. Drop me off someplace. Because I'm not—" James began to retort before Admiral Lethbridge-Stewart approached them and stunned James into silence with her presence alone. She was red in her face as she commanded complete attention and authority.

"Enough! What the commander says goes. We are going to the Citadel. You want out, Lieutenant? Then you can catch a ride back to Earth from the Citadel with a dishonorable discharge. Am I understood, Lieutenant." James was startled and snapped to attention immediately out of instinct. It dawned upon him that hia behaviour was unbecoming and managed to retain some of his composure.

"Yes, ma'am."

The Admiral nodded, seemingly satisfied. Her attention quickly returned to Shepard "Commander, effective immediately, the SSV Normandy is back under your command. Welcome back to the Alliance Navy." Shepard snapped into an attentive salute, the Admiral nodded with a ghost of a smile on her face before she turned about and left.

"Commander." Said a voice through the comm, it belonged to Flight Lieutenant Jeff Moreau, otherwise known as Joker. Shepard responded with some delight "Joker, that you?"

"Alive and kicking. I got an emergency transmission from Admiral Hackett for you." Joker responded before directing the message to the nearby consol. Display Admiral Hackett leaning over to a screen which was suffering heavily from static.

"Shepard… -stained heavy loses… -my force overwhelming… no way that we can defeat conventionally…" Admiral Steven Hackett voiced through the council. Shepard responded with informing his superior officer of his orders. "Anderson has already ordered me to the Citadel to talk with the Council."

"First I need you to— alliance outpost on mars- before losing control of the system—" Hackett said, despite the static and the distance. He still commanded a huge authority which had Shepard snapping to a salute. "Yes, sir."

"— researching prothean archives with Doctor T'soni-… found a way to stop the reapers- only way to stop them- contact soon, Hackett out." The Head of Alliance Navy continued before finishing the transmission. He obviously had a fleet to reorganize.

"Joker, set a course for the Mars Archives." Shepard ordered through the coms to the flight deck of the CIC. "Mars? Roger that."

"This is loco." James muttered under his breath, apparently shocked of the attack. Ashley handled herself better as she forwarded her question. "Why mars? What does he even think we'll find there?"

"I don't know yet but if it helps us win this war." Shepard responded, "Grab your gear, we're on the clock."

Shepard proceeded with putting on his N7-grade Armor. Top of the line with support capabilities and formidable kinetic barriers. It felt good to be serving aboard an Alliance vessel again. The armory was where it should be, in the shuttle bay. He was pleasantly surprised him with the N7-grade arsenal. He picked a N7 Valkyrie Assault Rifle with an Omni-blade bayonet attached underneath the attached high-velocity muzzle. It was a joy to see his M-11 Wraith Shotgun onboard. It was a rare variant of the M-22 Eviscerator whose exterior was that of tarnished gold. It had seen him through the Suicide Mission through the Omega-4 Relay. He secured a M-6 Carnifax Hand Cannon to his thigh as a sidearm before he boarded the shuttle.

Jack Harkness was much to Shepard's appreciation, fully dressed with N7-grade Armor. He brandished a N7 Hurricane SMG along with a N7 Valiant Sniper Rifle. They were soon joined by Ashley and James whom both were armed with M-99 Saber Semi-Automatic Assault Rifles. Ashley had additionally a M-5 Phalanx Heavy Pistol as a sidearm while James carried a M-27 Scimitar Assault Shotgun. Shepard gave Harkness a meaningful look, they were going to talk once they were done at Mars. It was impossible for him to be up so soon after his injury. The most puzzling aspect was the rate of his recovery. He had been brutally scarred with a most gruesome conplexion but now he looked like it had never happened in the first place. Sure, it would make a ludicrous story of a N7 Marine fighting on Earth completely naked and nothing but his training and a M-8 Avenger Rifle.

The doors to the shuttle closed as James took the pilot seat, flying them out of Normandy's Shuttle Bay while they secured their helmets. Next stop, the Mars Archives.

 **…**

The Doctor was indignate, Nardole managed to tune in to the Alliance News Network and the footage alone made his blood boil. They had made it personal. He navigated the TARDIS through real space, harassing the abominable hybrid vessels and disrupted their sensors. Something which gave the orbiting fleet a slim fighting chance despite having been reduced to half-strength. The defenses had been broken almost instantly. It was more of a slaughter than a war. He spotted something, he recognized it as the SSV Normandy, the sight almost made him giddy. I didn't take long for him to realize that they were heading for the Mars Archives.

He had no time waste and pulled a lever which returned the TARDIS to the time vortex. The central column moved while the reassuring sound of the TARDIS wheezed and groaned.

Once it ceased, he examined the screen to check the outside environment. It was safe, the perception filter was alive and kicking. "Nardole, wait in the TARDIS." The Doctor said, the timid man only managed to nod in response. He was supposed to look after the Doctor, not to endanger himself in a war.

The Doctor left the TARDIS, looking down the long corridor with an equally long glass window facing the tram station. He immediately knew that something was wrong when he heard the gunfire. Everything just had to violent and complicated. He then noticed humans in a heavy armor with a white and yellow colour pattern. Their weapons were raised and aimed at the Time Lord who didn't even blink at their presence. Why was humans fighting one another when their home and species were endangered?

Nevertheless, he didn't allow himself to be intimidated. The Doctor walked towards them, his eyebrows narrowed while he scolded them. "Hello, I'm the Doctor. I suggest that you do the smart thing, and take me to your leader."

The two armored troops exchanged worried glances, reluctantly with gesturing with their weapons for him to come along with them. The Doctor frowned as one took point while the other watched the rear. Moving onwards to what hededuced to be the tram station. He expected a really good explanation from whomever thought fighting amongst themselves was a good idea.

…

 **Author's Note:**

Unlike the last story, the Doctor won't be using an Omni-tool. It's inferior in comparison with his sonic screwdriver. He won't be using any guns, neither will he deviate by using armor or anything similar. He's the Doctor afterall. Naturally, I kept Jack Harkness doing the same thing here as he did in the previous version. Fighting the Reaper ground forces with nothing but a M-8 Avengers Rifle, all the while being naked.


	5. Mars without Martians

**A few hours ago**

Liara creased her brow into a frown. There was a new file of data in the Archive. How come that she didn't notice this before? She was all alone, had the archives all to herself as she browsed through the files on a monitor. She accessed the file, and to her surprise. She saw a man on the display. Liara would describe his appearance as gaunt with his thin-face and that tousled-mop of hair in the silvery shade of grey. He had a hooked nose and big ears. However, what captivated her was the intense silverly blue eyes framed by unruly, expressive eyebrows. "Hello Doctor T'soni. We've not met yet, I'm the Doctor."

The man said, addressing her directly. She was on full alert now, was this a recent addition to the archives? "How is this possible?" She murmured, quickly making her analysis of the file. The coding was rudimentary but unlike anything she has ever seen and it had somehow remained hidden in the archives.

"Oh, that's simple. Time travel. You're going to save this file on your Omni-tool and give it to me when we first meet." He explained like if it was something rudimentary. She shook her head.

"This isn't possible."

"Once you eliminate the impossible, whatever remains, no matter how improbable, must be the truth." He responded flatly, quoting Sir Arthur Doyle's Sherlock Holmes. Liara thought it was insane but she had to admit that it made some sense. Time travel.

"If you can travel in time, why can't you stop the Reapers from invading. Or prevent them from being created." She was definitively going insane if she was expecting a response from a recording.

"It doesn't work like that, I'm a part of the events taking place which means I can't go back without making a paradox. Granted, it's already a paradox. A bootstrap paradox provided that you give this message to me whenever you meet me."

She was absolutely vivid. He answered her question perfectly. This was real, it wasn't a trick. It couldn't possibly be a trick.

"Are you a human from the future?" She knew the question was ridiculous but had to ask anyway.

"No, I'm a Time Lord. I look human, or rather humans looks like Time Lords. It doesn't matter. What matters right now, is that if you're recieving this message then it means that the perception filter has expired." Liara somehow couldn't help but shiver the longer she felt those silverly blue eyes upon her. It was almost scrutinizing and outright impossible. "That means that you're running out of time. The Reapers will very soon invading and it's about get very dangerous at the Archives."

Every fiber of her being tensed as it dawned upon her that she had run out of time. Then she relaxed, he did mention that she was going to give this file to him when they meet which means that she'll live. However she would be foolish to rely on his words alone.

"What do I have to do?" She asked, her inquisitive mind saving her ever growing list of questions for later.

Liara then noticed the gleam in the Doctor's eyes while he smiled like some mischievious child.

…

"Normandy Actual to Badwolf One. I've tried to reach Mars on secure channels. No one is answering. How copy, over?" Joker said through their earpieces. Shepard's brow creased into a frown. There was no jamming of their communications; otherwise he wouldn't still be in contact with the Normandy.

"Solid copy Normandy Actual. Any sign of Reaper activity? Over." Shepard asked, having a sinking feeling that trouble was ahead of them.

"Negative, Badwolf One. No Reaper activity detected, over." Joker responded flatly. Could the communications array have been destroyed? "Be advised Normandy-One. The base appears to be online. Proceed with caution, the facility may be compromised." EDI chimed in through their coms with her feminine voice, picking up where Joker left off.

"Greyhound One to Badwolf Leader, your mission has not changed. Your priority is to locate and extract Doctor T'soni along with the intelligence she has acquired." Admiral Lethbridge-Stewart added, acting as their intelligence operator. "Weapons are free, you may engage and terminate hostiles with extreme prejudice at your discretion."

"Solid Copy, Greyhound One. We'll proceed with caution. Normandy Actual, keep me posted and standby for extraction."

"Roger that, Normandy Actual out."

"We're almost there." Vega voiced from the pilot seat with Jack Harkness acting as the Co-Pilot. The Kodiak came to a stop as it touched down. Vega and Harkness joined them while they performed their last minute check of their equipment. "Still no contact from the base but we got a massive storm heading our way."

"How long until it hits?" Shepard asked while his suit sealed itself while the kodiak pressurized in preparation for Extra-vehicular Activity. A last minute check where he loaded his weapons and made sure that it was green across the board.

"We got half an hour tops, after that there'll be difficulties to keep up comms with the Normandy." James answered, inserted a thermal clip into his M-99 Saber.

"Understood. Comms check everyone." Shepard said, activating his squad coms. One by one they acknowledged their callsigns; Shepard as Badwolf One with Ashley Williams designated as Badwolf Two. James Vega as Badwolf Three and Jack Harkness as Badwolf Four.

"All systems are a go. The Light is Green."

Shepard announced, knocking the end of his palm against the big button next to the door which opened with a light chime as a green light filled the interior of the Kodiak. They exited the Kodiak with their weapons ready and spread out with their rifles raised and aimed at all vectors. Everyone chimed in affirmatives that the landing zone was clear. Despite the circumstances, Shepard found comfort that he was with an Alliance unit. This is where he was meant to be. Mars, the red planet was sure a sight to behold with the red-tinted soil, craters and rock formations. Solar panels gleaming as they absorbed sunlight, converting it to energy.

Shepard took point with Vega while Williams and Harkness watched their rear while they advanced. "Damn, that's a huge storm. Looks a lot bigger in person." Vega commented once they spotted the approaching clouds of dust which covered the entire horizon, Shepard had to admit that it was huge.

"Come on, Lieutenant. It's not that bad." Ashley teased over the comms. Shepard almost decided to order them to cut the chat but thought better of it. They needed to cope with the Reaper invasion in their own way, even if it made seem more unprofessional.

"Doesn't mean it can't kill us."

"I'm more worried about the war back on Earth. Or the fact that nobody here is reporting back in."

"Fair Enough." James conceded while they approached to the ledge and vaulted down. They all took a knee as they raised their rifles in all directions. "What's that?", Shepard looked over at the location which Vega pointed out.

"Williams, check it out." His order was acknowledged. When they got closer, he couldn't help but feel his stomach twist. A squad of Alliance marines, all dead. They took a more defensive stance while Williams used her Omni-tool to make her assessment.

"Alliance. Sergeant Reeves, didn't put up much of a fight." The data conveyed through the Omni-tool wasn't reassuring. Their armor had ruptures and they didn't seem to have been able to fire a shot if their cool thermal clips was anything to go by. "Something isn't right here."

"Stay sharp and keep a low profile until we've identified the hostiles." Shepard commanded, there was no argument. They were soldiers, they advanced steadily with their weapons at the ready. The silence on secure channels and the verification of a dead squad had putt hem on high alert. There would be trouble and whatever they faced would've to be assumed to be hostiles. Then they heard it, gunfire.

Quickly moving to cover as they peeked over. They spotted armored men in the colour of yellow and white with a weapon trained at the frontal lob of an Alliance marine on his knees with the hands behind his head. He pulled the trigger, and the alliance marine collapsed with a big hole through the helmet. Shepard's grip on the weapon grew tighter in anger.

"Hostile Contacts, five of them. Pick your targets, fire on my mark then focus fire on the last one standing." He ordered silently through the comms. It was a clear shot, four of them were dead with ruptured armor and shredded kinetic barriers before they realized what happened; the fifth barely had time before being shot down aswell.

They heard more footsteps from behind the van which he now saw had the Cerberus logo, four or five at most. James took initiative and lobbed a grenade which put a quick end to the threat. They started to advance again but now moving from cover to cover in a staggered formation.

"Those were Cerberus weren't they." It was James and it was more of a statement than a question.

"Affirmative." Shepard responded curtly, he had identified the logo on the hostile's armor, verifying it was Cerberus.

"What's Cerberus doing here on Mars?" The tone was nothing short of a sublte accusation. That even Ashely even thought that he would abandon the Alliance in favor of Cerberus wounded him.

"Good question." Shepard retorted instantly, hoping it would be an end to it. If only it were so easy.

"You don't know?" She was skeptical of his answer, he could understand her disposition but this wasn't the right time for that conversation.

"Negative, I'm not with them anymore Ash, if that's what you're asking."

"It wasn't. But you've to admit, it's a bit convenient." She was right, it was convenient. They advanced, they spotted a few squads of cerberus troops digging themself in just outside the airlock. There was three vans, each carrying the cerberus logo. Shepard frowned, they were too few. It would require at the very least, a full battalion to capture the facility.

"Split up. Pincer Movement. Badwolf Two and Four. Badwolf Three with me." His order was perfectly executed. Their pincer movement quickly caught the Cerberus troopers in a crossfire. Harkness and Williams from one side, with Vega and Shepard from the other.

"Clear!" The Alliance soldiers chimed in one by one in confirmation, all hostiles had been eliminated.

"Doesn't look like they came here in force." Vega astutely observed.

"Indeed, it would require at the very least, a full battalion to capture this facility." Shepard added, voicing his analysis from before.

"Kind of suggest they had help, from the inside." Ashley said, the accusation more evident by the minute as they proceeded to enter the facility through the airlock. Slowly compensating the pressure and ventilation for a smooth transistion towards a more artifical environment. "I need a straight answer, Shepard."

"Ash—" Shepard said, turning to face her but was rudely interrupted.

"Don't 'Ash' me." Ashley blurted out with a finger on his chest. All traces of professionalism gone. "Do you know anything about this? What is Cerberus doing here?" Her accusation wasn't so subtle anymore.

"What makes you think that I know what they are up to?" Shepard's response was curt, inquisitive as his expression hardened. Emotions was obviously clouding her judgment, he had to admit that he wasn't far off either.

"You worked for them. How am I supposed to believe that you've cut all ties?"

"We joined forces to take down the Collectors, that's it." He responded firmly, not budging on the subject. Technically he didn't have to argue and just order her to be silent. Yet that would be problematic considering that they used to be involved.

"They rebuilt you from scratch. They gave you a ship, resources—" Shepard interrupted, his stare becoming all the more intense underneath the visor of his helmet.

"Let me be clear, I've had no contact with Cerberus after I destroyed the Collector Base. And I've no idea why they're here now or what they want."

"Commander Shepard has been under constant surveillance since coming back to Earth. No way have they been communicating since." Vega chimmed in, verifying Shepard's statement. It was sure good to know atleast someone trusted him

"Sorry, Shepard. I just—" Ashley said while realizing that she overstepped. She was obviously a bit embarrassed about it and unable to finish the sentence. Shepard's expression softened but he wasn't pleased in the slightest. He removed his helmet, looking straight into her eyes."You of all people should know what I'm about, Ash." His remark hit home. Ashley averted his gaze. Perhaps he was a bit harsh but they couldn't afford to be divided. "Please, trust me."

Harkness took point with Vega. Their weapons raised, they weren't expected. No hostiles in sight. Shepard and Williams took the rear with their weapons at the ready.

"I do." She said while they checked the corners of the maintenance bay. Shepard could tell that she had her doubts. "it's just that—" However, before they even could finish the sentence. They started to hear crawling sounds from the air vents, there was gunfire as they quickly proceeded to take position.

Suddenly the lid was kicked open and an Asari dressed in a white synthetic fabric dropped down and vaulted from the elevated area. Turning around as she flicked her hand while being enveloped by a blue hue of what was easily identified as biotics.

The two Cerberus troopers whom had pursued her, vaulted down after her but was instead caught in her singularity; an artificial gravity field imitating a black hole by pulling everything caught in its sphere of influence into a single point where the sheer pressure reduced materials to atoms.

The Asari raised her p M-5 Phalanx Heavy Pistol and fired several rounds encased with Wrap energy which caused a rather explosive reaction. She fired a few additional rounds into their bodies just to be sure that they were dead.

Vega had his rifle trained on her while they approached. Shepard put a hand on the muzzle and tapping it downwards. "Easy there, Lieutenant. She's with us."

Liara turned to face them and beamed with a smile. "Shepard. Thank the goddess you're alive." her voice was soothing. Shepard couldn't help but smile. "I was worried when the reports came in. They hit Earth hard?" she asked with a quizzical expression upon Jack Harkness whom approached her.

"Captain Jack Harkness." He spoke smoothly as he gently grasped her hand and bent over to kiss it like a gentlemen, making Liara's cheeks to turn indigo. She was blushing.

However their interaction was interrupted by a liberate cough from Ashley. "Yeah… it was difficult to leave." Liara seemed to snap back to reality as she gently walked over to embrace her comfortly in a friendly hug.

"Ashley, I'm sorry." Her voice was smooth, reassuring and Ashley eased a bit. Smiling at the comforting words of a friend. "But… why'd come here?" She added as she broke the hug, looking at the rest of them.

"Hackett ordered us to come. Said that you'd know what's going on." Shepard said, smiling cordially at Liara whom beamed at him with confidence.

"I do." She answered smugly while they walked over to a nearby window.

"Hallelujah, some answers. Finally." James said, speaking for the rest of them. They were really in need of good news.

"Maybe, I've found two things of interest, the first being plans for a Prothean device. One that potentially could be used against the Reapers." Liara answer as she looked at Shepard after making her clarification. "The other thing is actually a person, someone called the Doctor."

"There are files on the Doctor in the Archives?" Harkness asked, his forehead creased into a frown. Liara looked at him with a tilted head.

"Just vague references here and there, plenty of allegories and contradicting statements. It's evidently however is that the Protheans were afraid of him. Besides thay, the most concrete is the message he left me." Jack Harkness' eyes went wide, a stupid grin forming on his face.

"The Doctor left you a message?" The sudden change of Jack's tone caught Shepard off-guard. It was almost giddily, like if he was a teenager with a crush. Liara perked a brow, showing a loopsided smile in amusement at the sudden change of attitude.

"I take it that you know him?" Liara asked, the tone was mild. She was probing for information.

"Without him, I wouldn't be here today." He answered cryptically. "However, I do think we've more pressing matters."

"Quite right, Captain." Liara answered, still smiling. Shepard could tell that Liara was enjoying the attention and somewhat eccentric behaviour of the Captain. "In any case, my work here paid off. The Archives is full with data. An overwhelming amount."

Shepard frowned, it was too good to be true. "I believe it when I see it. Where will we find this weapon?"

"It's not a weapon, not yet. Its plans for a device, a blueprint." Liara's explanation was sound. Although, putting all their faith into one device didn't sit right with him. It would be a gamble, considering that they didn't actually know of its functions.

"It's more than we had a minute ago. How do we get to it?"

"The Archives are just across that tramway. Assuming Cerberus has not locked it down."

Well, that complicated things. However, it didn't make any sense. Why would Cerberus be fighting them while they could combine their resources to fight the Reapers?

"What are they after?"

James decided to chim in, "Yeah, they seem hell-bent on capturing you."

"They want what I'm here for, what we're all here for."

"But why?"

"The Protheans came close to defeating the Reapers. They had plans to destroy them but ran out of time."

"And anything powerful enough to destroy the Reapers." Ashley inserted while Jack finished with. "Just might be something Cerberus would be interested in."

"So, it's a race to the archives?" Vega asked until they suddenly heard the sound of more troopers and a weld searing through the door's lock.

"Heads up! We got company. Liara sync with our comms. Your designation is Badwolf Five." Shepard proclaimed.

"Bring it on." James said with a smirk while they took positions. They would be at a disadvantage with Cerberus having the high ground.

"Not this time, Vega." Shepard to Vega's disappointment.

"What?" Vega exclaimed in slight disbelief, his discipline lapsing briefly.

"Get back to the shuttle. If Cerberus beat us to the archives then I need you to cover the exits."

"But—"

"That was an order, Lieutenant." The command quickly got the marine to return to his more disciplined self and complied with the direct order from his superior officer. He had just put his helmet on before engaging the pressurization sequence of the airlock. Meanwhile, the rest of the Badwolves were ready to fight their way to their objective.

…

The Doctor looked around him, taking every nook and cranny he could spot. The Cerberus operatives were quite stoic and didn't even retort at any of his attempt at small-talk. Something about them rubbed him the wrong way, it was like if they were drones.

They had just reached the tram station where he spotted more Cerberus operatives but one stood out. A woman in a catsuit. What could've fooled others didn't fool him as he got closer. She wasn't breathing. That in itself implied that she wasn't a human. In fact, he hazard a guess that she was an Android.

The Doctor saw the creased forehead, recognizing a frown. "This man ain't in the personal roster. Identify yourself if you want to live." She demanded, the sound of gunfire could be heard from the trams.

"Wrong, the only reason I'm standing before you is because I wanted to talk directly to the head of this operation. That's you, isn't it?" The Doctor retorted, smirking mischievously. The operative scowled, aiming her M-4 Shuriken submachine gun at his forehead.

"I give you to the count of three before I…"

"You do what, pull the trigger?" He challenged. "You won't do that, because you want to know how I got into this facility without your knowledge. Furthermore, I can tell that you're aren't really human."

That statement gave Doctor Eva Coré pause, moving her finger to her ear as she rapidly asks in almost a synthetic manner while still holding the gun steady "Orders?"

It seems like the puppeteer had direct oversight over what Cerberus was doing here. He or she is no doubt a control freak if the stoic and drone-like behaviour of the troops was anything to go by. The Doctor knew that he had played his cards right when the gynoid lowered the firearm. "The Illusive Man would like to speak with you, follow me or be put down. Your choice."

The Doctor didn't feel any rush, time was relative afterall. Her attempt to intimidate only made him loft s brow. He would play their game, having this Illusive Man fall into a trap of false confidence.

"Set up a perimeter. No one else comes across." The gynoid commanded to a Cerberus Centurion once they were across.

"We still have teams on the other side." The centurion voiced as the gynoid halted, the two facing each other as she spoke with clear authority. "No one! And shut down those cameras."

With those words, she lifted the submachine one and shot one of the surveillance cameras. They continued on as they walked by a console unit. The Doctor flicked his wrist and the sonic screwdriver chimed lowly as he quickly swirled it about, tuning it with appropriate settings.

Fortunately, the gynoid failed to notice. She apparently didn't think him capable of meddling with anything on such a short notice. Cereberus clearly underestimated him as many others have done. Coming through the checkpoint, he stared in brief awe of the prothean databank at the center of the chamber.

...

Their aims were true as they advanced through the family, clearing room by room. The Cerberus troopers were fearless, unrelentling and thoroughly disciplined which peaked Jack's interest. He had known that the organization had rapidly grown over the past few months but he didn't expect them to have drilled squads this soon.

Shepard illuminated with a blue hue of his biotics; charging through solid matter and clash right into a Centurion whom was thrown back by the impact and broke his neck upon hitting the wall. Shepard then pointed the barrel of his M-11 Wraith Shotgun at s nearby trooper and fired before he turned about to strike another trooper with his biotic imbued gauntlet. The visor cracked as did the cranium as it hit the table, sliding down the floor in a dripping pool of blood.

The suppressing fire from Jack and Hasley kept them pinned while Liara bombarded them with biotics. They have fought their way ever since they rendevouz with Liara. Cerberus seem inclined to stop them, no matter the cost. Question is naturally, why. They had to find an alternate path through a room which had gone through a decontamination process, while there were people inside. The sight was revolting. That and that open airlock which suffocated the personnel in the mess hall. This took ruthless efficiency to the extreme.

They had learned from a terminal that a Doctor Eva Coré was behind the despicable act; a complete disregard for life. Liara ultimately felt responsible for not noticing.

The decontaminated room had been used for the study of prothean data and artifacts. Unfortunately, they didn't have time to go through any of it. The clock was ticking, well outside the room into a corridor with a long window following the entire walk way. If it wasn't for the present circumstances, he wouldn't mind admiring the view.

"That's the tram line. It'll take us straight to the Archives. No doubt Cerberus will have it locked down, hopefully we can override it at the security station." Liara's voice echoed in the long corridor. They started to walk it down until Jack Harkness suddenly came to a halt. He knew that feeling, it was that of a perception filter.

He glanced to the corner of his eye, to the place he didn't want to look and stared in wonder. His eyes went wide while letting out a childish cheer. The others turned about to see what Jack was excited about and just dropped their jaws when they saw it. "That's the TARDIS! Oh beautiful TARDIS!"

Jack dashed to a blue box, reminding them all about the red phone boxes in London. There were square windows on all sides which seemed to have been covered by curtains from the inside. The doorway was blocked by dual doors, one with each window and a single handle and a lock.

Jack grasp around the box to the best of his ability and plant a kiss on the door. Joyful at the sight. Shepard's forehead creased into a frowned, had Harkness gone mad?

"What's that?" Ashley asked a bit curious.

"It's a TARDIS. His TARDIS!" Jack shouted in a happy manner as he turned around to face the questioning looks.

"Who's?" Shepard said as his curiosity took over. Although, he could probable guess.

"The Doctor's! He's here!"

The belief of The Doctor being a tall tale was slowly washing away. Shepard had been skeptical ever since Earth but the more evidence he saw. He stared in awe, maybe there was hope. Maybe it all didn't depend on him?

They kept pushing onwards, reaching the end of the walkway. "The Tram Station is through this door."

Shepard touched the omni-door panel, the door slid open and they came face to face with a dual piped machine turret hanging from the roof, turning and aimed at time before sprayed controlled bursts their way. Fortunately, Shepard quickly dashed to cover as Liara shouted out for them to look out.

"Is that the only way in?" Ashley asked in a slight disbelief. Liara shook her head and as she reached for the intercom panel.

"Override code Doctor Disco. Shut down turret." Liara spoke and the turret stopped firing. "The Doctor said that I would know when to use that override."

The smugness in her voice only made Jack grin all the more wider. They caught the remaining Cerberus troops guarding the station off-guard and made short work of them. Liara sat down, her digits quickly typing series of codes. They caught the recent surveillance footage on a nearby monitor. It was Doctor Eva Coré giving orders before she shot the camera. However what caught Shepard's attention was the elderly man dressed in a velvet coat being escorted like a prisoner by two troopers.

"That's the Doctor. I recognize him from the message that he sent, or rather will leave for me." Liara said while her digits were at work. "Looks like they've arrived to the Archives."

"And it looks like they won't send a tram anytime soon." Ashley commented.

"Can you override it?" Shepard asked a bit puzzled but Liara just shook her head. "The Archives is on a separate network, we're completely locked out."

Ashley didn't seem that disheartened as an idea popped up in her head. "Not completely, what if we can find a short-range transmitter. Helmet to helmet. And then we convince them that we're with them, and the Alliance forces has been taken care off."

"Good idea, let's see what we can find." It didn't take long for them to find a dead Centurion. Ashley was crouching and fiddling with the helmet.

"He's got a transmitter in his helmet if I could just…" The rest of her sentence died when the visor slid open. The face underneath was pale, gaunt with a tint of blue to his complexion. A cord ran from the temple to behind the cranium. The eyes were artificial, hollow like if their very humanity had been replaced by tech. "Oh god, he looks like a husk."

It was a revolting sight to be sure. Yet despite the similarities, his skin showed no decay. "Yeah, not quite. But they've definitively done something to him." He voiced as he inspected the face further, seems like the Illusive Man had some implants operated into him, or rather every trooper. Reaching out to grasp the helmet to helmet transmitter.

"Engineered, by Cerberus!" Ashley was indignate. "They claim to stand for humanity, yet they do this to their own people."

Her gaze reverted back to Shepard, a scrutinizing stare which wasn't exactly unwarranted. "That could've been you, Shepard. For all I knew, that's what Cerberus had done to you."

Shepard rose to face her, narrowing his eyes. This was the second time she was second-guessing him. "How can you compare me with that thing, do I look like a husk to you Lieutenant-Commander."

The words coming through his mouth seem to shake her, not expecting such an answer. She shook her head. "No, Shepard. I just…"

"Enough, put your personal feelings aside for now. We'll talk after the mission. Have I made myself clear?"

Only silence followed as she nodded, falling back to the military doctrine they were so familiar with, "Yes, sir."

"Good." He muttered as he brought the com to his mouth, voicing. "Hello. This is Delta Team. Anybow there?"

"Where the hell have you been? Nevermind. What's your status?" came a harsh and malicious voice through the comm, same muffled voice they've heard all over from the troopers.

"At the tram station, waiting extraction. All hostiles terminated." Shepard voiced, the voice muffler must work both ways to ensure anonymously between the troops.

"Roger that. Echo Team will ride over and secure the station."

A smile formed on his lips, things were turning around for them and they saw in the distance of how the tram was heading their way. Time will tell what's going on the other side.

...

The Doctor stood before the virtual display of the prothean databank. The omni-based terminal illuminated the dimly lit chamber. His sonic screwdriver buzzed over the terminal briefly, "Beautiful." he said in admiration.

"Hello, Doctor." A voice said from behind, The Doctor turned about and came face to face with a holographic image. He saw a smartly dressed man in an exclusive synthetic suit with a cigarette between his fingers. Two artificial eyes and hair which may once have been considered, dashing.

"You're the Illusive Man." The Doctor said, more of a statement than a question. The illusive man just nodding. "Correct, I must say that your deduction skill is impressive. You saw through what have fooled the Alliance for weeks."

The Doctor scoffed, "She kept recycling oxygen to imitate breathing." Even a Dalek Sleeper drone was more convincing.

"Like I said, impressive." The Illusive man said, exhaling some smoke. "Your brilliance is undeniable. You've a ship which can appear and disappear anywhere."

"If you want my TARDIS then you can forget about it." The tone of broke no argument. The Illusive Man took another drag from his cigarette.

"You're missing the point. The Protheans, a most fascinating race left all this for us to discover, but we've squandered it." He began to speak, exhaling more smoke. "The archives has been left to gather dust for thirty years. All of this time and only now, there's been significant progress."

He's a good orator, The Doctor admit that. However, not as good as Winston Churchill. He'd teach this fellow something about speeches. "The archives jumpstarted the technological advancement of mankind by several centuries. Granted, it was at the expense of innovation."

"Exactly, your ship. Your knowledge. The Data in these artifacts are the key to solving the Reaper Threat. The Alliance will undoubtedly destroy the Reapers. I say, why destroy when we can control?" The way it was presented felt like a sale's pitch. It made his patience wear thin. It started to come together. Control.

"Is that why your troops are no better tham drones following orders?" The Doctor respoded distastefully.

"They've been improved." The Illusive Man answered cryptically. Improved, like a cyberman was an upgrade. "The Reapers, with your knowledge. We can dominate them, use their power. Harness their very essence to bring humanity to the apex of evolution."

The Doctor's eyebrows rose and narrowed into dangerous archs. His forehead creased into a frown while his eyes stared with such intensity that the Illusive Man involuntary shiver. "You're delusional. A megalomaniac. Your entire species are at risk and you decide to make a grab for power."

The Illusive Man took another exaggerated drag from his cigarette "A pity." He then nodded and the Cerberus troopers along with the gynoid trained their weapons on him. They pulled the triggers, yet nothing happened.

"Funny thing about mass accelerated weapons." The Doctor said with a grin, "If you reverse the polarity and instead imcrease the density, it jams instead." The cigarette slipped through the Illusive Man's fingers, his cybernetic eyes grew wide. However before anyone could say anything. The door to the tram station opened ans in came four people with their guns trained against the Cerberus personnel. Then there was gunfire, the troopers fell to the ground, dead. The gynoid tried to grab the Doctor but he simply sit out of the way, deftly grasping around the wrist and twisted it into an angle while throwing her over his hip to the ground. The sonic screwdriver buzzed and it was disabled. However the Doctor wasn't happy with the outcome.

"Shepard." The Illusive Man said, both as a greeting while sticking to the facts.

"You, shush!" The Doctor said indignant to the Cerberus Leader before turning towards Commander Shepard and his fireteam. "And you, I hope that you're proud of yourself. You just killed two disarmed drones of this megalomaniac."

To say they were startled was an understatement. "I believe that—"

"I said shut up!" The Doctor roared, cutting the Cerberus Leader off. "You're not out of the woods, Mister Illusive. Far from it, I'm giving you a chance to cease with your bid for power and human dominance! One chance before I make you and your Cerberus' existence a living hell!"

There was an unerving silence in the room as everyone present shivered. This was the indignant fury of the Doctor, risk it at your own peril.

"Now, considering that we're still in a pickle. The Harvest won't stop itself." The Doctor continued, turning about and approached the terminal to the databank with Liara rushing up to collect the data.

Ashley held her firearm trained on the hologram, despite that he wasn't there or posed a threat. Her scowl didn't hide the hatred she bode for him. "Illusive man?"

"The same." He answered smugly.

"What do you want?"

"What I've always wanted."

"The domination of mankind." Jack Harkness scolded the Illusive man who just cast him a nonchalant glance.

"Nevertheless, Lieutenant-Commander Ashley Williams. You've a lot to thank Shepard for during his time with Cerberus. Not only did he supply us with valuable intel on the Reapers by going through the Omega-4 Relay but also improved the public relations throughout the Terminus Systems."

He obviously pushed the right buttons, Ashley seemed to be boiling with anger. Smiling smugly as Shepard also took the bait. "I destroyed the Collector Base with my team."

"Speaking of which, how is your beloved XO, Miss Lawson doing?"

"Your what?!" Ashley voiced in a menacing tone as she glanced to her right at the Commander. No longer in the role of a soldier, more like an angry and jealous ex-girlfriend. The Illusive Man smirked triumphantly before the image flickered and vanished.

The Doctor and Liara turned about to see Ashley now shouting at Shepard. "Who the hell is Lawson!"

"What is it with you humans fighting one another." The Doctor scolded, was about to report but the Time Lord's scowl made the words get stuck in her throat. "Stop acting like children throwing tantrums. Harkness, you should've known better." That was as much acknowledgement which he was going to get before the Doctor turned his attention back to the terminal.

"You got a lot of explaining to do, once we're back on the Normandy." Ashley whispered to Shepard with a clenched fist.


End file.
